- a method to identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment

If you wish to align plant sequences, please use the specialized GeneSeqer server at PlantGDB

Follow steps 1 - 4 or click on Help or Tutorial for more detailed instructions:

      Step 1:    Select splice site model
      Step 2:    Input genomic DNA sequence
      Step 3:    Select or input cDNA/EST sequences
      Step 4:    Select alignment stringency level
      Step 5:    Submit job

STEP 1: Select splice site model

Species (selects species-specific splice site model)

STEP 2: Input genomic DNA sequence

Sequences should be in the one-letter-code ({a,b,c,g,h,k,m,n,r,s,t,u,w,y}), upper or lower case; all other characters are ignored during input. Multiple sequence input is accepted in FASTA format (sequences separated by identifier lines of the form “>SQ;name_of_sequence comments”) or in GenBank format.

Paste your genomic DNA sequence here:

... or upload your sequence file (specify file name):

... or type in the GenBank accession number of your sequence:

Select format: plain FASTA GenBank
Sequence name: (optional, used in plain sequence format only)
From position: to position: Strand: original reverse both

STEP 3: Select or input cDNA/EST sequences

Spliced Alignment: The output will show an optimal threading of a significantly matching cDNA/EST sequence into the genomic DNA by aligning putative exons only and displaying putative introns as (long) gaps in the cDNA/EST.

Select pre-processed EST database OR paste your own cDNA/EST sequence(s) here ( FASTA format ):

... and/or upload your cDNA/EST sequence file (specify file name):

STEP 4: Select alignment stringency level

Select "alignment stringency level" allowed user to select parameter to GeneSeqerWS. "Strict" invokes "-x 30 -y 45 -z 60", moderate "-x 16 -y 24 -z 48", and low "-x 12 -y 12 -z 30" argument to GeneSeqerWS.

Select alignment stringency level: strict moderate low

STEP 5: Submit job

Select "Submit" to send the job to the server. By default, output will be posted to your browser. You may select to have the ouput sent to you by email instead. Selection of this option is advised in the rare case that output posting is slow due to server overload.

Click here to send the output to this email address:
HTML formatted output [default: simple text].This option will not work if your mailer wraps long lines.

BCB @ ISU

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